Entering edit mode
Nitesh Turaga
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50
@nitesh-turaga-6112
Last seen 10.2 years ago
Hi,
I'm a little stuck with the charm analysis using MeDip arrays. It
started
with an error at "readCharm" and trickled into the finer details of
what
information the function needed.
I have seen the previous question in
https://stat.ethz.ch/pipermail/bioconductor/2012-February/043719.html
.
Here, the user built a custom ".pos" file. But the ".pos" file i'm
using
is from nimblegen and so is the ".ndf". I do not have a column in
which
"experimental" or otherwise is mentioned.
My .pos file looks like this,
PROBE_ID SEQ_ID CHROMOSOME POSITION COUNT LENGTH GC
CHR01FS000015738 chr1:15366-44081 chr1 15738 3 50
0.68
CHR01FS000016058 chr1:15366-44081 chr1 16058 2 50
0.70
CHR01FS000016770 chr1:15366-44081 chr1 16770 5 50
0.54
And my .ndf file looks like this.
PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID
PROBE_SEQUE
NCE MISMATCH MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS
PROBE_ID PO
SITION DESIGN_ID X Y DMD
537151_1_25 BLOCK1 interval rank target_tm:76.00;probe_tm:77.60;freq:
9.25;count:01;rules:0000;score:0812 chr19:6588109-6599163
AAAAGACCAGAAAACAG
GGCACGGACGTAAGCAGAGAGGTTCTATGTGTC 0 254819035 254819035 25 1
CHR19FS006590
155 6590155 537151 1 25 A03
537151_1_27 BLOCK1 interval
rank
target_tm:76.00;probe_tm:75.70;freq:10.71;count:01;rules:0000;score:08
28 chr5:83677266-83688611
GGAGTTACATATCCTTATCAAATCCCAGGCATTAATGCAAGTAAATTGC
AACCCATACG 0 254968001 254968001 27 1 CHR05FS083677686 83677686
537151 1 2
7 A03
> ndf = list.files(".",pattern = ".ndf",full.names = TRUE)
> pos = list.files(".",pattern = ".pos",full.names = TRUE)[1]
> files = list.files("Lung Cancer/2.1M/XYS",pattern =
".xys",full.names =
>T)[1]
> pkg = new("NgsTilingPDInfoPkgSeed",ndfFile = ndf, xysFile =
>files,posFile = pos, author = "Nitesh Turaga",email =
>"nturaga at andrew.cmu.edu <mailto:nturaga1 at="" jhmi.edu="">",biocViews =
>"DNAMethylation",genomebuild = "NCBI Build 36",organism =
"Human",species
>= "Homo Sapiens")
> makePdInfoPackage(pkg,destDir=".")
======================================================================
=====
=====
Building annotation package for Nimblegen Tiling Array
NDF: 100929_HG19_Deluxe_Prom_Meth_HX1.ndf
POS: 100929_HG19_Deluxe_Prom_Meth_HX1.pos
XYS: 542585A01_Sample12_2013-06-27_12-16_2013-07_532.xys
======================================================================
=====
=====
Parsing file: 100929_HG19_Deluxe_Prom_Meth_HX1.ndf... OK
Parsing file: 100929_HG19_Deluxe_Prom_Meth_HX1.pos... OK
Merging NDF and POS files... OK
Parsing file: 542585A01_Sample12_2013-06-27_12-16_2013-07_532.xys...
OK
Creating package in ./pd.100929.hg19.deluxe.prom.meth.hx1
Inserting 30291 rows into table featureSet... OK
Inserting 0 rows into table pmfeature... Error in
sqliteExecStatement(con,
statement, bind.data) :
bind.data must have non-zero dimensions
> traceback()
8: stop("bind.data must have non-zero dimensions")
7: sqliteExecStatement(con, statement, bind.data)
6: sqliteQuickSQL(conn, statement, bind.data, ...)
5: dbGetPreparedQuery(conn, sql_template, bind.data = data)
4: dbGetPreparedQuery(conn, sql_template, bind.data = data)
3: dbInsertDataFrame(conn, "pmfeature", parsedData[["pmFeatures"]],
tiledRegionPmFeatureSchema[["col2type"]], !quiet)
2: makePdInfoPackage(seed, destDir = ".")
1: makePdInfoPackage(seed, destDir = ".")
> sessionInfo()
R version 2.15.2 Patched (2013-02-08 r61876)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
[3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
[5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
attached base packages:
[1] tools stats graphics grDevices datasets utils
methods
[8] base
other attached packages:
[1] RColorBrewer_1.0-5 limma_3.14.4 genefilter_1.40.0
[4] pdInfoBuilder_1.22.0 affxparser_1.30.2 RSQLite_0.11.2
[7] DBI_0.2-5 ff_2.2-10 bit_1.1-9
[10] oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0
[13] BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] affyio_1.26.0 annotate_1.36.0 AnnotationDbi_1.20.3
[4] BiocInstaller_1.8.3 Biostrings_2.26.3 codetools_0.2-8
[7] foreach_1.4.0 GenomicRanges_1.10.6 IRanges_1.16.4
[10] iterators_1.0.6 parallel_2.15.2 preprocessCore_1.20.0
[13] splines_2.15.2 stats4_2.15.2 survival_2.37-2
[16] XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.4.0
NOTE:
I am doing the above process because this was the error I encountered
before. This is the specific error I was getting and there was no
package
called pd.100929.hg19.deluxe.prom.meth.hx1.
>files = list.files("XYS/")
> fileNames = list.files("XYS/")
> rawData = readCharm(files = fileNames, path ="XYS/",ut =
"_532.xys",md =
>"_635.xys")
Loading required package: pd.100929.hg19.deluxe.prom.meth.hx1
Attempting to obtain 'pd.100929.hg19.deluxe.prom.meth.hx1' from
BioConductor website.
Checking to see if your internet connection works...
Package 'pd.100929.hg19.deluxe.prom.meth.hx1' was not found in the
BioConductor repository.
The 'pdInfoBuilder' package can often be used in situations like this.
Error in read.xysfiles2(channel1 = file.path(path, files2Ut), channel2
=
file.path(path, :
Must install the pd.100929.hg19.deluxe.prom.meth.hx1 package.
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE,
logical.return = TRUE, :
there is no package called ?pd.100929.hg19.deluxe.prom.meth.hx1?
I read the pdInfoBuilder package reference, charm reference. I am not
able
to find a reply to solve this problem.
I could use the help.
Thank you,
Best,
Nitesh
--
Nitesh Turaga
MS in Computational Biology
Carnegie Mellon University
--
Nitesh Turaga
MS in Computational Biology
Carnegie Mellon University
